title: luminal progenitor type rep4

data_processing:
Reads containing adapters/ with low quality were trimmed using cutadapt (v4.2), -m 30
Trimmed sequence reads were mapped against hg19 using bowtie2 (2.3.5.1)
Read count extraction was performed in R using countOverlaps (GenomicRanges)
Assembly: mm10

source_name: luminal progenitor

growth_protocol: luminal wild type

extract_protocol:
mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using trypsin (Gibco) and dispase (Stemcell) treatments. Luminal progenitor and mature cells were sorted via FACS based on EpCAM, CD49f, cKit and CD14 surface markers. RNA was extracted using Rneasy Plus Micro kit (Qiagen). 500 pg of RNA was used for cDNA amplification using NEB Kit #E6421 "NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification"
RNA-Seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770/E7775) according to the manufacturer's protocol. 8 cycles were used to amplify the libraries.

treatment_protocol: Wild type mice, no specific treatment

value: luminal progenitor


title: DO203_ORSAM19451_GT21-08453_M_heart

status: Public on May 24 2024

type: SRA

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Assembly: GRCm38
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Diversity Outbred mice were sensitized on a high-fat, high-sugar (HFHS) diet

tag: tissue

value: heart

tag: diet

value: 45% fat


title: luminal differentiated  type rep4

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

source_name: luminal differentiated

tag: strain

tag: cell type

value: luminal differentiated

tag: genotype

value: wild type


title: luminal differentiated  type rep3


title: DO200_ORSAM19448_GT21-08444_M_heart


title: DO201_ORSAM19449_GT21-08377_M_heart


title: shTRPS1.32_rep1_GEX

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed by the cellranger pipeline using default settings.
Assembly: mm10

source_name: mammary gland

extract_protocol:
Mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0.25% trypsin  (Gibco) and 5 mg/mL dispase (Stemcell) treatments. Cells were incubated with 0.5 µg of TotalSeq antibodies (anti-EpCAM, anti-CD49f, 118237 and 313633 from Biolegend)
10x Genomics scRNA-Seq was performed using the Chromium single cell 3’ assay v3 as recommended by the manufacturer.

treatment_protocol: Mice were given doxycycline supplemented food (625 mg/kg, ssniff) for 10 days to induce the expression of the shRNA (shTrps1.32/shTrps1.34 or shRenilla control depending on the animal genotype).

value: mammary gland

value: shTRPS1.32 ki/+; CAG-rtTA3 tg/+

value: EpCAM-enriched cells


title: DO199_ORSAM19447_GT21-08579_M_heart


title: DO197_ORSAM19446_GT21-08404_M_heart


title: luminal progenitor type rep2


title: luminal progenitor type rep3


title: DO195_ORSAM19444_GT21-08565_M_heart


title: luminal progenitor type rep1


title: luminal differentiated  type rep1


title: shTRPS1.34 rep4

source_name: luminal: GFP+ mKATE2+

extract_protocol:
Mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0.25% trypsin (Gibco) and 5 mg/mL dispase (Merck). GFP+ mKate2+ shRNA-expressing luminal and basal cells were sorted via FACS using EpCAM and CD49f surface markers (antibodies 12-9326-42 from eBioscience and 313631 from Biolegend). RNA was extracted using Rneasy Micro Plus Kit (Qiagen). 600 ng of RNA was used for cDNA amplification using the NEB Kit #E6421 "NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification"
RNA-Seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770/E7775) according to the manufacturer's protocol. 8 cycles were used for library amplification.

treatment_protocol: Mice were given 5 injections of tamoxifen (75 mg/kg body) on 5 consecutive days to induce recombination of the CAG-lsl-RIK locus by CreER specifically in Krt8-expressing mammary epithelial cells. They were then fed with doxycycline supplemented food (625 mg/kg, ssniff) for 10 days to induce the expression of the shRNA (shTrps1.32/shTrps1.34 or shRenilla control depending on the animal genotype).

value: luminal:GFP+ mKATE2+

value: shTRPS1.34 ki/+; ROSA26-CAG-LSL-RIK ki/+; K8-CreERT2 tg/+


title: DO193_ORSAM19442_GT21-08524_M_heart


title: shTRPS1.34 rep2


title: DO196_ORSAM19445_GT21-08421_M_heart


title: shTRPS1.34 rep3


title: DO191_ORSAM19440_GT21-08543_F_heart


title: DO192_ORSAM19441_GT21-08622_M_heart


title: DO190_ORSAM19439_GT21-08621_M_heart


title: shTRPS1.32 rep1

value: shTRPS1.32 ki/+; ROSA26-CAG-LSL-RIK ki/+; K8-CreERT2 tg/+


title: DO189_ORSAM19438_GT21-08439_M_heart


title: DO188_ORSAM19437_GT21-08465_M_heart


title: shRen rep5

value: shRen ki/+; ROSA26-CAG-LSL-RIK ki/+; K8-CreERT2 tg/+


title: shRen rep4


title: shTRPS1.34 rep1


title: shTRPS1.32 rep2


title: DO185_ORSAM19434_GT21-08420_M_heart


title: luminal differentiated  type rep2


title: DO186_ORSAM19435_GT21-08563_M_heart


title: DO187_ORSAM19436_GT21-08528_M_heart


title: DO184_ORSAM19433_GT21-08619_M_heart


title: shRen rep2


title: shRen rep1


title: DO183_ORSAM19432_GT21-08437_M_heart


title: DO194_ORSAM19443_GT21-08484_M_heart


title: basal wild type rep5

source_name: luminal

extract_protocol:
mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0.25% trypsin (Gibco) and 5 mg/mL dispase (Merck). Wild type luminal and basal cells were sorted via FACS based on  EpCAM and CD49f surface markers (antibodies 12-9326-42 from eBioscience and 313631 from Biolegend). RNA was extracted using Rneasy  kit (Qiagen).  1 ug of RNA was used for library prep.
RNA-Seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770/E7775) according to the manufacturer's protocol.

treatment_protocol: wild type mice

value: luminal


title: DO182_ORSAM19431_GT21-08440_M_heart


title: DO181_ORSAM19430_GT21-08600_M_heart


title: DO180_ORSAM19429_GT21-08393_M_heart


title: luminal wild type rep4

source_name: basal

value: basal


title: basal wild type rep4


title: DO179_ORSAM19428_GT21-08472_M_heart


title: DO178_ORSAM19427_GT21-08450_M_heart


title: DO177_ORSAM19426_GT21-08426_M_heart


title: luminal wild type rep3


title: basal wild type rep3


title: basal wild type rep2


title: DO176_ORSAM19425_GT21-08488_M_heart


title: shRen rep3


title: basal wild type rep1


title: DO175_ORSAM19424_GT21-08415_M_heart


title: luminal wild type rep1


title: luminal wild type rep2


title: DO172_ORSAM19421_GT21-08458_M_heart


title: DO173_ORSAM19422_GT21-08636_M_heart


title: shRen luminal rep6

extract_protocol:
Mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0.25% trypsin (Gibco) and 5 mg/mL dispase (Merck). GFP+ mKate2+ shRNA-expressing luminal and basal cells were sorted via FACS using EpCAM and CD49f surface markers (antibodies 12-9326-42 from eBioscience and 313631 from Biolegend). RNA was extracted using Rneasy Plus Micro kit (Qiagen).  The whole amount of RNA from each sample was used for library prep.
RNA-Seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770/E7775) according to the manufacturer's protocol. 14 cycles were used for library amplfification.

value: shRen ki/+; ROSA26-CAG-rtTA3-IRES-mKATE2 tg/+

tag: treatment

value: shRen


title: DO171_ORSAM19420_GT21-08431_M_heart


title: shRen luminal rep5


title: DO170_ORSAM19419_GT21-08558_F_heart


title: shRen basal rep5


title: DO169_ORSAM19418_GT21-08367_F_heart


title: DO168_ORSAM19417_GT21-08378_F_heart


title: luminal wild type rep5


title: shRen basal rep4


title: shRen luminal rep4


title: DO167_ORSAM19416_GT21-08414_F_heart


title: DO166_ORSAM19415_GT21-08560_F_heart


title: shRen basal rep3


title: shRen luminal rep3


title: shTRPS1.34 luminal rep2


title: DO163_ORSAM19412_GT21-08397_F_heart


title: DO165_ORSAM19414_GT21-08553_F_heart


title: DO162_ORSAM19411_GT21-08620_F_heart


title: shTRPS1.34 basal rep2


title: DO164_ORSAM19413_GT21-08638_F_heart


title: shTRPS1.32 luminal rep1


title: DO174_ORSAM19423_GT21-08583_M_heart


title: shRen luminal rep2


title: shRen basal rep2


title: DO160_ORSAM19409_GT21-08546_F_heart


title: DO161_ORSAM19410_GT21-08616_F_heart


title: shTRPS1.32 basal rep1


title: shRen basal rep6


title: DO158_ORSAM19407_GT21-08573_F_heart


title: shRen luminal rep1


title: DO157_ORSAM19406_GT21-08526_F_heart


title: DO159_ORSAM19408_GT21-08614_F_heart


title: DO156_ORSAM19405_GT21-08514_F_heart


title: shTRPS1.34 basal rep1


title: shRen basal rep1


title: DO155_ORSAM19404_GT21-08446_F_heart


title: DO154_ORSAM19403_GT21-08398_F_heart


title: DO153_ORSAM19402_GT21-08482_F_heart


title: DO151_ORSAM19400_GT21-08492_F_heart


title: DO152_ORSAM19401_GT21-08479_F_heart


title: DO148_ORSAM19397_GT21-08603_F_heart


title: DO150_ORSAM19399_GT21-08578_F_heart


title: DO149_ORSAM19398_GT21-08628_F_heart


title: DO147_ORSAM19396_GT21-08537_F_heart


title: shTRPS1.34 luminal rep1


title: DO145_ORSAM19394_GT21-08581_F_heart


title: DO146_ORSAM19395_GT21-08521_F_heart


title: DO142_ORSAM19391_GT21-08604_F_heart


title: DO144_ORSAM19393_GT21-08388_F_heart


title: CD4Tcells-HFD-16hrstim-5

type: RNA

city: Toronto

first: Brendan

last: Cordeiro

state: Ontario

address: 209 Victoria St.

department: Keenan Research Center

country: Canada

institute: St-michael's hospital

description: Gene expression data from sorted naïve CD4+ T cells from mice fed NCD or HFD for 4 weeks

hyb_protocol: Each sample was hybridized to a GeneChip Mouse Gene 2.0 ST array (Affymetrix) for 16- 18 h at 45 °C

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Data were analyzed using GeneSpring software (Version 12.1, Agilent) and was summarized using the ExonRMA16 algorithm followed by quantile normalization.

label: Biotin

source_name: CD4+ T cells, sorted, spleen/Lymph node

label_protocol: Biotin Allonamide Triphosphate, performed by SickKids Microarray facility, Toronto, Canada

growth_protocol: Naïve CD4+ T cells (CD4+ CD44low-int) were magnetically isolated by negative selection from spleens and lymph nodes

extract_protocol: Total RNA was then isolated (RNEAsy, Qiagen). Total RNA quality was analyzed by RNA 6000 Pico LabChip on a 2100 BioAnalyzer (Agilent).

treatment_protocol: Cells were plated on TC-treated 96 well plates and stimulated with 2ug/ml plate-bound anti-CD3 and anti-CD28 antibodies for 16hrs.

tag: agent

value: Spleen/Lymph node

value: High-Fat diet


title: DO143_ORSAM19392_GT21-08368_F_heart

value: heart


title: CD4Tcells-HFD-16hrstim-4


title: DO141_ORSAM16110_GT21-08513_F_heart

value: 45% fat


title: DO140_ORSAM16109_GT21-08587_F_heart


title: CD4Tcells-HFD-16hrstim-1


title: CD4Tcells-HFD-16hrstim-3


title: DO138_ORSAM16108_GT21-08566_F_heart


title: CD4Tcells-HFD-16hrstim-2


title: CD4Tcells-NCD-16hrstim-2

value: Normal chow


title: CD4Tcells-HFD-Nostim-3


title: CD4Tcells-NCD-16hrstim-3


title: DO137_ORSAM16107_GT21-08470_F_heart


title: CD4Tcells-NCD-16hrstim-1


title: DO133_ORSAM16106_GT21-08483_F_heart


title: CD4Tcells-HFD-Nostim-4


title: CD4Tcells-HFD-Nostim-5


title: CD4Tcells-NCD-16hrstim-4


title: CD4Tcells-HFD-Nostim-2


title: CD4Tcells-NCD-Nostim-4


title: CD4Tcells-HFD-Nostim-1


title: DO132_ORSAM16105_GT21-08633_F_heart


title: HeLa CTSB-kd B

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description:
CTSB-kd 2
HeLa Lyso samples - all data normalized

data_processing:
Strand NGS for alignement, quantification and normalization
Assembly: ENSEMBL GRCh38.p5
Supplementary files format and content: gene expression normalized per gene

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: DMEM + 10% FBS + 1% P/S

extract_protocol:
TrueSeq RNA Sample Preparation Kit (Illumina, Netherlands) was used to prepare samples for NGS analysis. Accurate quantitation of cDNA libraries was performed by using the QuantiFluorTM dsDNA System (Promega, Germany). The size range of cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp).
cDNA libraries were amplified and sequenced by using the cBot and HiSeq 1000 from Illumina (SR, 1×50bp).

tag: cell line

value: HeLa cells

value: CTSB-kd

value: DMEM+10percent FBS + 1percent  P/S

tag: group

value: lysosomal defect


title: HeLa CTSB-kd A

description:
CTSB-kd 1
HeLa Lyso samples - all data normalized


title: DO131_ORSAM16104_GT21-08408_F_heart


title: CD4Tcells-NCD-Nostim-2


title: HeLa GAA-kd B

description:
GAA-kd 2
HeLa Lyso samples - all data normalized

value: GAA-kd


title: DO130_ORSAM16103_GT21-08480_F_heart


title: CD4Tcells-NCD-Nostim-1


title: HeLa UQCRC1-kd B

description:
UQCRC1-kd 2
HeLa mito samples - all data normalized

value: mitochondrial respiratory chain deficiency


title: HeLa GAA-kd A

description:
GAA-kd 1
HeLa Lyso samples - all data normalized


title: HeLa UQCRC1-kd A

description:
UQCRC1-kd 1
HeLa mito samples - all data normalized


title: DO128_ORSAM16101_GT21-08532_F_heart


title: DO129_ORSAM16102_GT21-08567_F_heart


title: DO126_ORSAM16100_GT21-08423_F_heart


title: HeLa scrambled B2

description:
scrambled B2
HeLa mito samples - all data normalized
HeLa Lyso samples - all data normalized

value: scrambled

value: control


title: DO125_ORSAM16099_GT21-08510_F_heart


title: DO124_ORSAM16098_GT21-08406_F_heart


title: HeLa scrambled A2

description:
scrambled A2
HeLa mito samples - all data normalized
HeLa Lyso samples - all data normalized


title: DO123_ORSAM16097_GT21-08547_F_heart


title: DO120_ORSAM16094_GT21-08390_M_heart


title: DO121_ORSAM16095_GT21-08588_F_heart


title: DO119_ORSAM16093_GT21-08409_M_heart


title: HeLa scrambled A1

description:
scrambled A1
HeLa mito samples - all data normalized
HeLa Lyso samples - all data normalized


title: DO118_ORSAM16092_GT21-08478_M_heart


title: Patient 9, Fresh

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Fastq files were aligned using Hisat2 alinger (version 2.2.1) to the human genome (GRCh38) obtained from Ensembl
Gene counting was then performed using featureCounts function in subread (version 2.0.1) with Ensembl annotations (Homo_sapiens.GRCh38.105.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all samples

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy micro kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using protocol published in Katayama et.al (BMC Genomics, 2015) for STRT RNA sequencing.

value: ovary

tag: culture

value: Fresh


title: Patient 2, LN221, IVA

value: IVA


title: DO115_ORSAM16090_GT21-08438_M_heart


title: Patient 8, Fresh


title: Patient 11, Fresh


title: DO116_ORSAM16091_GT21-08503_M_heart


title: Patient 10, Matrigel, IVA

value: Matrigel


title: DO113_ORSAM16088_GT21-08471_M_heart


title: DO112_ORSAM16087_GT21-08615_M_heart


title: DO111_ORSAM16086_GT21-08396_M_heart


title: DO109_ORSAM16085_GT21-08562_M_heart


title: Patient 9, Matrigel, Fragmentation

value: Fragmentation


title: HeLa scrambled B1

description:
scrambled B1
HeLa mito samples - all data normalized
HeLa Lyso samples - all data normalized


title: Sirpα-/- glomeruli

city: Nanjing

first: QIAN

last: BIN

state: JiangSu

address: 639 Longmian Avenue

department: School of Life Science and Technology

country: China

institute: State Key Laboratory of Natural Medicines

description: Gene expression after  in glomeruli from Sirpa-/- mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner (G5761A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.   Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: glomeruli;Sirp-alpha-/-

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).    Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: For the isolation of glomeruli, the renal cortex was cut into small cubes of ~1 mm3 and digested with HBSS solution containing collagenase D (1 mg/ml, Sigma-Aldrich, C6885), protease (1 mg/ml, Sigma-Aldrich, P6911) and DNase I (1 U/ml, Sigma-Aldrich, D5025) for 15 min at 37 °C. The digested tissue was screened through a 100 μm filter. Glomeruli containing Dynabeads were gathered using a magnetic particle concentrator. Adding 1ml Trizol (Vazyme, China) to each sample and extracting RNA according to the manufacturer's recommended protocol.

treatment_protocol: The wild type (WT) and podocyte specific SIRPα knockout (Sirpa-/-) mice were received a single intraperitoneal injection of 0.5 ml pristane respectively, and monitored for 4 months to construct experimental LN mice. Podocytes were isolated from pristane-treated WT and Sirpa-/- mice for further analysis.

tag: gender

value: male

value: glomeruli

tag: age

value: 8 month


title: Patient 9, LN221, Fragmentation


title: DO122_ORSAM16096_GT21-08455_F_heart

value: heart

value: 45% fat


title: DO108_ORSAM16084_GT21-08561_M_heart


title: Patient 10, Fresh


title: DO107_ORSAM16083_GT21-08462_M_heart


title: Patient 8, LN221, IVA


title: Patient 4, Fresh


title: Patient 7, Fresh


title: Patient 3, Fresh


title: Patient 2, Fresh


title: DO106_ORSAM16082_GT21-08591_M_heart


title: DO104_ORSAM16080_GT21-08380_M_heart


title: DO114_ORSAM16089_GT21-08505_M_heart


title: DO103_ORSAM16079_GT21-08504_M_heart


title: Patient 6, Fresh


title: Patient 8, Matrigel, IVA


title: WT glomeruli

description: Gene expression after  in glomeruli from WT mice

source_name: glomeruli;WT mice


title: CD4Tcells-NCD-Nostim-3

value: Spleen/Lymph node

value: Normal chow


title: Patient 1, Fresh


title: DO101_ORSAM16077_GT21-08624_M_heart


title: DO102_ORSAM16078_GT21-08468_M_heart


title: Patient 10, LN221, IVA


title: Patient 5, Fresh


title: Patient 4, Matrigel, IVA


title: DO099_ORSAM16075_GT21-08618_M_heart


title: DO098_ORSAM16074_GT21-08413_M_heart


title: DO100_ORSAM16076_GT21-08382_M_heart


title: Patient 3, Matrigel, Fragmentation


title: Patient 2, Matrigel, IVA


title: DO097_ORSAM16073_GT21-08441_M_heart


title: Patient 6, Matrigel, IVA


title: Patient 1, Matrigel, Fragmentation


title: DO096_ORSAM16072_GT21-08463_M_heart


title: DO105_ORSAM16081_GT21-08609_M_heart


title: Patient 5, Matrigel, IVA


title: DO095_ORSAM16071_GT21-08435_M_heart


title: DO094_ORSAM16070_GT21-08551_M_heart


title: Patient 4, LN221, IVA


title: Patient 3, LN221, Fragmentation


title: DO092_ORSAM16068_GT21-08556_M_heart


title: Patient 1, LN221, Fragmentation


title: DO091_ORSAM16067_GT21-08602_M_heart


title: DO089_ORSAM16065_GT21-08606_M_heart


title: J_Lat

city: New York

first: Ganjam

middle: V

last: Kalpana

state: NY

address: 1300, Morris Park Ave.,

department: Genetics

institute: Albert Einstein Collge of Medicine

data_processing:
The libraries were sequenced using Illumina NextSeq 500 (Illumina, San Diego, CA, USA) to obtain pair-end sequencing of 27 bp (read1) × 100 bp (read2) and a single index 8bp in length.
Cell Ranger software version 3.1.0 (10X Genomics, Pleasanton, CA, USA) was used to align and count to the reference genome and transcripts.
Assembly: Human genome (GRCh38) and HIV-1HXB2 complete genome (GenBank K03455.1) were merged for alignment.
Supplementary files format and content: Tab separated value files and matrix files

source_name: J-Lat

growth_protocol: The latent T-cells ACH2, J1.1, and J-Lat were maintained in RPMI-1640 (HyClone; Cat# SH30096.01) supplemented with 2 mM L-glutamine (Gibco; Cat# 25030-081), 100 U/ml penicillin, 100 µg/ml streptomycin (Gibco; Cat# 15140-122), 10% fetal bovine serum (Atlas Biologicals; Cat# F-0500-A) and 10 mM HEPES (Sigma; Cat# H0887).

extract_protocol:
Briefly, the latent T-cells ACH2, J1.1, and J-Lat were revived in RPMI-1640 (HyClone; Cat# SH30096.01) supplemented with 2 mM L-glutamine (Gibco; Cat# 25030-081), 100 U/ml penicillin, 100 µg/ml streptomycin (Gibco; Cat# 15140-122), 10% fetal bovine serum (Atlas Biologicals; Cat# F-0500-A) and 10 mM HEPES (Sigma; Cat# H0887). After 2 passages, the cells were split in the respective medium 1 million cells/ml and then cells were submitted to Einstein Genomics facility for scRNA-Seq.
Single-cell mRNA libraries were built using the Chromium Next GEM Single Cell 3’ Library Construction V3 Kit according to the manufacture's protocol.

treatment_protocol: These are uninduced cells without any treatment.

value: J-Lat

value: HIV-R7/E-/GFP infected Jurkat cells

value: WT

value: No treatment


title: DO093_ORSAM16069_GT21-08495_M_heart


title: DO086_ORSAM16062_GT21-08447_M_heart


title: HDMB03_PPHLN1_3

first: Liam

middle: D

last: Hendrikse

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Aligned with STAR v2.5.2b
Assembly: Hg19
Supplementary files format and content: count matrix (txt. File)

source_name: T Milde et al., J Neurooncol 2012

growth_protocol: Tumorspheres were grown in StemPro NSC Serum-Free Medium on ultra-low attachment tissue culture plates

extract_protocol:
Total RNA was extracted from all samples using the Norgen RNA extraction kit (Norgen Biotek),
Library constructed with NEB Ultra II directional RNA library prep kit with poly-A selection module

value: Human HDMB03 group 3 medulloblastoma cell line

value: PPHLN Morpholino


title: ACH_2

value: HIV-1 latent T cell clone with one integrated proviral copy.


title: HDMB03_PPHLN1_2


title: HDMB03_PPHLN1_4


title: HDMB03_PPHLN1_1


title: DO084_ORSAM16060_GT21-08416_M_heart


title: DO090_ORSAM16066_GT21-08490_M_heart


title: DO085_ORSAM16061_GT21-08548_M_heart


title: HDMB03_Ctrl_4

value: scramble control


title: J1_1

value: HIV-1 LAV infected Jurkat E6 Cells (J1.1)


title: HDMB03_Ctrl_2


title: DO081_ORSAM16057_GT21-08384_M_heart


title: HDMB03_Ctrl_3


title: DO082_ORSAM16058_GT21-08570_M_heart


title: HDMB03_Ctrl_1


title: DO079_ORSAM16055_GT21-08534_M_heart


title: DO078_ORSAM16054_GT21-08399_M_heart


title: OA_Mf_P5_Veh_18409_resequence

city: Nijmegen

first: Cheng

last: Wang

address: Geert Grooteplein 28

department: Molecular biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Paient 5 OA-Mf were treatment without TA, only DMSO as control.

data_processing:
Preprocessing of reads was performed with seq2science v0.1.0 . Genome assembly hg19 was downloaded from UCSC with genomepy v0.8.3. Paired-end reads were trimmed with trim galore! v0.6.4  and cutadapt with default options. Reads were aligned with hisat2 v2.1.0 .
Mapped reads were removed if they did not have a minimum mapping quality of 44, were a (secondary) multimapper or aligned inside the ENCODE blacklist. Afterwards, duplicate reads were marked with picard MarkDuplicates v2.21.2 . Read counting and summarizing to gene-level was performed on filtered bam files using featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: TPM files of RNA expression.

source_name: Osteoarthritis paient Mf

growth_protocol: Synovial tissue from end-stage OA patients was obtained after joint replacement surgery. Post-operative biopsies from patients with end-stage OA were handed over to the experimental rheumatology department of the RIMLS. The synovial tissue was separated from muscle, fat and ligament tissue and cultured overnight in RPMI1640 with 10% FCS at 37 ℃ to let monocytes from a vascular origin leach out of the synovial tissue. Next, the suspension was washed, run through a 70 µm cell strainer, after which the  and the digestionenzymes were inactivated  reaction was stopped by adding pure FCS. Erythrocytes were removed using lysis buffer (155 mM NH4Cl, 12mM KHCO3 and 0.1 mM EDTA). To remove erythrocytes, a red blood cell lysis buffer was added and the reaction was later stopped by PBS addition. To isolate CD14+ cells, MACS buffer (PBS, 1.5% ACDA, 1% FCS) and CD14 microbeads were added to the sample, which was then run through a MACS (Magnetic-Activated Cell Sorting) column. After five washing steps, CD14 cells were eluted following the manufacturer’s instructions and resuspended in a 6 cm dish in RPMI medium supplemented with 10% FCS. As a positive control for the TA response, PBMC from a healthy blood donation buffy coat were exposed to TA under the same culture conditions using the same set of reagents and equipment.

extract_protocol:
RNA was extracted using Trizol and  RNEasy mini kit, including an on-column DNase I digestion.
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems)

treatment_protocol: Osteoarthritis paient OA-Mf and healthy donor PBMCs are treated with a final concentration of 1 micromolar TA (triamcinolone acetonide, Sigma, T6501) or only DMSO solvent (0.1% final concentration) lasted 4 hours.

value: OA-Mf

tag: library

value: RNA-seq


title: DO088_ORSAM16064_GT21-08599_M_heart


title: DO076_ORSAM16053_GT21-08533_M_heart


title: PBMC_TA_18418_resequence

description: PBMCs were treatment 1 micromolar TA for 4 hours.

source_name: PBMC

value: PBMC


title: OA_Mf_P5_TA_18408_resequence

description: Paient 5 OA-Mf were treatment 1 micromolar TA for 4 hours.


title: DO087_ORSAM16063_GT21-08371_M_heart


title: DO075_ORSAM16052_GT21-08442_M_heart


title: OA_Mf_P4_Veh_18411_resequence

description: Paient 4 OA-Mf were treatment without TA, only DMSO as control.


title: OA_Mf_P3_Veh_18413_resequence

description: Paient 3 OA-Mf were treatment without TA, only DMSO as control.


title: DO072_ORSAM16049_GT21-08535_M_heart


title: DO073_ORSAM16050_GT21-08611_M_heart


title: DO074_ORSAM16051_GT21-08626_M_heart


title: OA_Mf_P3_TA_18412_resequence

description: Paient 3 OA-Mf were treatment 1 micromolar TA for 4 hours.


title: OA_Mf_P2_TA_18414_resequence

description: Paient 2 OA-Mf were treatment 1 micromolar TA for 4 hours.


title: OA_Mf_P4_TA_18410_resequence

description: Paient 4 OA-Mf were treatment 1 micromolar TA for 4 hours.


title: DO071_ORSAM16048_GT21-08449_M_heart


title: DO070_ORSAM16047_GT21-08464_F_heart


title: DO080_ORSAM16056_GT21-08494_M_heart


title: PBMC_Veh_18419_resequence

description: PBMCs were treatment without TA, only DMSO as control.


title: DO068_ORSAM16045_GT21-08405_F_heart


title: OA_Mf_P1_Veh_18417_resequence

description: Paient 1 OA-Mf were treatment without TA, only DMSO as control.


title: DO069_ORSAM16046_GT21-08637_F_heart


title: OA_Mf_P1_TA_18416_resequence

description: Paient 1 OA-Mf were treatment 1 micromolar TA for 4 hours.


title: DO066_ORSAM16043_GT21-08445_F_heart


title: PBMC_Veh_18419


title: PBMC_TA_18418


title: DO065_ORSAM16042_GT21-08402_F_heart


title: OA_Mf_P5_Veh_18409


title: DO064_ORSAM16041_GT21-08569_F_heart


title: DO063_ORSAM16040_GT21-08564_F_heart


title: DO062_ORSAM16039_GT21-08639_F_heart


title: OA_Mf_P4_Veh_18411


title: OA_Mf_P4_TA_18410


title: OA_Mf_P2_Veh_18415_resequence

description: Paient 2 OA-Mf were treatment without TA, only DMSO as control.


title: OA_Mf_P3_Veh_18413


title: DO060_ORSAM16037_GT21-08522_F_heart


title: OA_Mf_P2_TA_18414


title: DO057_ORSAM16034_GT21-08634_F_heart


title: OA_Mf_P1_TA_18416


title: DO056_ORSAM16033_GT21-08545_F_heart


title: DO054_ORSAM16031_GT21-08555_F_heart


title: LPS_Mf_TA_rep3

description: LPS-Mf

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq.
Reads were mapped to human gene annotation using bowtie and mmseq (Ensemble release 72).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a gene.mmseq, containing counts per gene.

source_name: LPS primed monocyte drerived Mf were treated with  TA  for 4 hours

growth_protocol: Monocytes were isolated from healthy donors using density gradient centrifugation with Ficoll-Paque and followed by removal of T cells using an additional Percoll gradient. Isolated monocytes were purified using negative selection with beads of CD3, CD19 and CD56, yielding high purity (> 95%) monocytes.  After one-hour incubation, attached monocytes were differentiated toward macrophages in vitro culture in RPMI 1640 medium with added 10% human serum. Trained innate immunity macrophages were induced by treatment of monocytes with 5 μg/mL BG for 24 hours, followed by washout and extra 5 days in culture in RPMI pulsed 10% human serum. Similarly, tolerized macrophages were induced by treatment with 10 ng/ml LPS for 24 hours, followed by washout and extra 5 days in culture in RPMI pulsed 10% human serum.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
rRNA was depleted with RiboZero Kit. Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Trained innate immunity macrophages(BG-mf) and tolerized macrophages(LPS-mf) were stimulated with 100 mM triamcinolone acetonide (TA, Sigma, T6501), 10 ng/ml  LPS or combination of TA and LPS for 4 hours.

value: Monocyte-derived macrophages


title: DO059_ORSAM16036_GT21-08629_F_heart

value: heart


title: OA_Mf_P3_TA_18412


title: LPS_Mf_TA_rep2

description: LPS-Mf


title: DO067_ORSAM16044_GT21-08577_F_heart

value: 45% fat


title: DO055_ORSAM16032_GT21-08434_F_heart


title: OA_Mf_P1_Veh_18417


title: LPS_Mf_TA_rep1

description: LPS-Mf


title: DO053_ORSAM16030_GT21-08559_F_heart


title: OA_Mf_P5_TA_18408


title: DO051_ORSAM16028_GT21-08596_F_heart


title: LPS_Mf_TALPS_rep3

description: LPS-Mf

source_name: LPS primed monocyte drerived Mf were treated with TA and LPS  for 4 hours


title: DO061_ORSAM16038_GT21-08499_F_heart

source_name: heart


title: LPS_Mf_TALPS_rep2

description: LPS-Mf


title: DO050_ORSAM16027_GT21-08451_F_heart


title: LPS_Mf_TALPS_rep1

description: LPS-Mf


title: LPS_Mf_LPS_rep3

description: LPS-Mf

source_name: LPS primed monocyte drerived Mf were treated with  LPS  for 4 hours


title: DO048_ORSAM16025_GT21-08625_F_heart


title: OA_Mf_P2_Veh_18415


title: DO049_ORSAM16026_GT21-08433_F_heart


title: DO058_ORSAM16035_GT21-08610_F_heart


title: LPS_Mf_LPS_rep2

description: LPS-Mf


title: DO044_ORSAM16022_GT21-08527_F_heart


title: DO052_ORSAM16029_GT21-08544_F_heart


title: DO042_ORSAM16020_GT21-08512_F_heart


title: LPS_Mf_DMSO_rep3

description: LPS-Mf

source_name: LPS primed monocyte drerived Mf were treated with  DMSO (Veh control) for 4 hours


title: LPS_Mf_DMSO_rep2

description: LPS-Mf


title: LPS_Mf_LPS_rep1

description: LPS-Mf


title: DO040_ORSAM16018_GT21-08391_F_heart


title: DO041_ORSAM16019_GT21-08632_F_heart


title: BG_Mf_TA_rep1

description: BG-Mf

source_name: BG primed monocyte drerived Mf were treated with  TA  for 4 hours


title: DO046_ORSAM16023_GT21-08530_F_heart


title: BG_Mf_TA_rep3

description: BG-Mf


title: DO043_ORSAM16021_GT21-08369_F_heart


title: LPS_Mf_DMSO_rep1

description: LPS-Mf


title: BG_Mf_TALPS_rep3

description: BG-Mf

source_name: BG primed monocyte drerived Mf were treated with TA and LPS  for 4 hours


title: BG_Mf_TA_rep2

description: BG-Mf


title: DO038_ORSAM16016_GT21-08584_F_heart


title: DO037_ORSAM16015_GT21-08518_F_heart


title: BG_Mf_TALPS_rep1

description: BG-Mf


title: BG_Mf_LPS_rep3

description: BG-Mf

source_name: BG primed monocyte drerived Mf were treated with  LPS  for 4 hours


title: BG_Mf_TALPS_rep2

description: BG-Mf


title: DO039_ORSAM16017_GT21-08473_F_heart


title: DO035_ORSAM16013_GT21-08403_F_heart


title: DO034_ORSAM16012_GT21-08466_F_heart


title: BG_Mf_LPS_rep1

description: BG-Mf


title: DO047_ORSAM16024_GT21-08642_F_heart


title: BG_Mf_LPS_rep2

description: BG-Mf


title: DO033_ORSAM16011_GT21-08605_F_heart


title: BG_Mf_DMSO_rep3

description: BG-Mf

source_name: BG primed monocyte drerived Mf were treated with  DMSO (Veh control) for 4 hours


title: DO032_ORSAM19390_GT21-08515_F_heart


title: DO031_ORSAM19389_GT21-08448_F_heart


title: BG_Mf_DMSO_rep2

description: BG-Mf


title: BG_Mf_DMSO_rep1

description: BG-Mf


title: DO-420_M_Islet

data_processing:
Assembly: GRCm38
Supplementary files format and content: DO_RNAseq_islet_counts_matrix.csv
Supplementary files format and content: DO_RNAseq_islet_mrna_annots.csv
Supplementary files format and content: DO_RNAseq_islet_vst_matrix.csv
Islet: processed DO islet RNAseq data (legacy data, reprocessed with batch effects removed as reported in /RNAseq/Raw/GBRS/QTLViewer_setup/QTLv_format_ISLET_REMOVE_BATCH.R script).
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.
counts_matrix.csv: raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.
vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
mrna_annots.csv: gene annotation file ENSEMBL version 75.
QTLViewer: QTLViewer data object and documentation. QTLViewer object generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
GBRS_QTL2_genoprobs: final genoprobs on QTL2 format generated through GBRS for each tissue (used for genotype QCing). Genoprobs generated by the R script /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_genoprobs.R

source_name: pancreatic islet

value: pancreatic islet


title: DO030_ORSAM19388_GT21-08594_F_heart


title: DO027_ORSAM19386_GT21-08550_F_heart


title: DO-417_M_Islet


title: DO028_ORSAM19387_GT21-08540_F_heart


title: DO025_ORSAM19384_GT21-08392_F_heart


title: DO026_ORSAM19385_GT21-08419_F_heart


title: DO-414_M_Islet


title: DO-416_M_Islet


title: DO036_ORSAM16014_GT21-08635_F_heart


title: DO023_ORSAM19382_GT21-08506_F_heart


title: DO-412_M_Islet


title: DO-410_M_Islet


title: DO022_ORSAM19381_GT21-08456_F_heart


title: DO024_ORSAM19383_GT21-08511_F_heart


title: DO-415_M_Islet


title: DO-409_M_Islet


title: DO-408_M_Islet


title: DO-413_M_Islet


title: DO-407_M_Islet


title: DO083_ORSAM16059_GT21-08477_M_heart


title: DO021_ORSAM19380_GT21-08557_F_heart


title: KO1

city: Ann Arbor

first: Stephen

middle: J

last: Weiss

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

data_processing:
Reads were trimmed using Cutadapt v2.3. The reads were then evaluated using FastQC (v0.11.8) to determine the quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL) using STAR (v2.7.8a) and assigned count estimate to genes with RSEM (v1.3.3).
Alignment options followed ENCODE standards for RNA-seq and QC metrics from several different steps were aggregated by multiQC v1.7.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Expected gene counts in a tab deliminated txt file.

source_name: Primary Dermal Fibroblasts

growth_protocol: Murine priimary dermal fibroblasts were maintained in high glucose DMEM supplemented with 10% FBS & antibiotics in a humidified incubator with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol.
Libraries were prepped using NEBNext rRNA Depletion Kit (NEB, E6310) and NEBNext UltraExpress RNA Library Prep Kit (NEB, E3330).
The library was prepared for Total RNA-seq analysis and were subject to 151 paired end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol: Fibroblasts were cultured in 3D type I collagen hydrogels for 24 hours before isolation of RNA.

value: Primary Dermal Fibroblasts

value: 3D Type I Collagen Culture


title: DO-406_M_Islet


title: WT1

value: Control (wildtype)


title: KO2


title: WT2


title: DO-405_M_Islet


title: DO-404_M_Islet


title: DO-403_M_Islet


title: DO-411_M_Islet


title: DO-402_M_Islet


title: DO-401_M_Islet


title: Ovary, AMH, 4 hour

city: Boston

first: Ngoc Minh Phuong

last: Nguyen

state: MA

address: 55 Fruit st

department: Pediatric Surgical Research Laboratory

institute: Massachusetts General Hospital andHarvard Medical School

description: 10X Genomics

data_processing:
samples were aligned against the mouse reference transcriptome mm10-2020-A and analyzed using Seurat 1 (R version 4.2.0, Seurat version 4.1.0). A standard pre-processing workflow was applied independently to each sample. Samples were filtered based on a mitochondrial percentage under 20% and unique feature counts between 200 and 10,000. After normalization, samples were merged using the 'merge' function in Seurat. Conventional visualization and clustering methods were applied, and cluster-specific markers were identified with the ‘FindAllMarkers’ function in Seurat.
Assembly: mm10-2020-A
Supplementary files format and content: tab-separated values files and matrix files

source_name: Ovary

extract_protocol:
One ovary from each animal was collected in cold PBS, and the ovaries from each group (N = 5 per group) were cut into small pieces and placed in 2 mL of DMEM (10% FBS, 1% penicillin/streptomycin), supplemented with 21 U/mL of Papain (Worthington, LK003178) and 1 mg/mL of collagenase A (Sigma Aldrich, 10103578001), for 30 minutes at 37°C. After digestion, the cells were subjected to further mechanical digestion using the gentleMACS™ Dissociator (Miltenyi Biotec). Single cells were isolated by straining the digested tissue suspension through a 70-micron filter. The cells were then counted to assess cell viability and to obtain 10,000 cells from each group for library preparation.
Samples were processed for scRNAseq according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10× Genomics) and Chromium Controller (10× Genomics). Single-cell libraries were sequenced using the NovaSeq S4 (Illumina) by the Bauer Core Facility at Harvard University.

value: Ovary

value: AMH (0.75mg/kg)


title: FBC-Tumor2

city: Pittsburgh

first: Jing

last: Hu

address: 5117 Centre Ave

institute: Univeristy of Pittsburgh

data_processing:
Salmon V0.13.1
Assembly: mm10
Supplementary files format and content: Tab-delimited plain-text file includes raw counts and TPM for each sample

molecule: polyA RNA

source_name: FBC tumor in cecum

extract_protocol:
Total RNA was extracted from the cecal tissues of indicated mice using the RNeasy Mini Kit (Qiagen). After DNase I treatment and performing quality control (QC), 200 ng of high-quality total RNA was proceeded to library construction.
Oligo(dT) magnetic beads were used to isolate mRNA. The mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized using mRNA template and random hexamers primer. Short fragments are purified and resolved with EB buffer for end repair and single nucleotide A (adenine) addition. After that, the short fragments were connected to sequencing adapters. The double-stranded cDNA library was completed through size selection and PCR enrichment.

value: FBC tumor in cecum


title: FBC-Tumor3


title: Ovary, Doxorubixin, 4 hour

description: 10X Genomics

value: Doxorubicin (3mg/kg)


title: DO-400_M_Islet


title: FBC4-L2

source_name: Distal colon

value: Distal colon


title: FBC-Tumor1


title: DO-397_M_Islet


title: DO-398_M_Islet


title: FBC4-L1

source_name: Proximal colon

value: Proximal colon


title: DO-399_M_Islet


title: FBC4-C

source_name: Cecum

value: Cecum


title: FBC3-L2


title: DO-396_M_Islet


title: DO-395_M_Islet


title: DO-394_M_Islet


title: FBC3-L1


title: FBC2-L1


title: FBC3-C


title: DO-393_M_Islet


title: FBC2-L2


title: DO-392_M_Islet


title: DO-391_M_Islet


title: Ovary, Doxorubicin and AMH, 4 hour

description: 10X Genomics

value: Doxorubicin ((3mg/kg) and AMH (0.75mg/kg)


title: Ovary, Control, 4 hour

description: 10X Genomics

value: Controls (PBS/Saline)


title: FBC1-L2


title: DO-389_M_Islet


title: DO-390_M_Islet


title: FBC1-C


title: DO-388_M_Islet


title: BC4-L2

value: Villin-Cre;BRAFV600E/+ mice


title: FBC1-L1


title: DO-386_M_Islet


title: DO-385_M_Islet


title: DO-384_M_Islet


title: BC4-L1


title: BC4-C


title: BC3-L1


title: DO-383_M_Islet


title: BC3-C


title: BC3-L2


title: BC2-L2


title: DO-381_M_Islet


title: BC2-L1


title: DO-377_M_Islet


title: FBC2-C


title: BC2-C


title: DO-378_M_Islet


title: BC1-L2


title: DO-379_M_Islet


title: BC1-L1


title: DO-376_M_Islet


title: BC1-C


title: B4-L2

value: BRAFV600E/+ mice


title: DO-387_M_Islet


title: DO-373_M_Islet


title: DO-374_M_Islet


title: B4-L1


title: B4-C


title: DO-382_M_Islet


title: DO-371_M_Islet


title: B3-L2


title: B3-L1


title: DO-369_F_Islet


title: DO-380_M_Islet


title: DO-368_F_Islet


title: B3-C


title: B2-L2


title: DO-370_F_Islet


title: DO-367_F_Islet


title: B2-C


title: DO-366_F_Islet


title: DO-365_F_Islet


title: B1-L1


title: B2-L1


title: DO-363_F_Islet


title: B1-L2


title: DO-364_F_Islet


title: B1-C


title: DO-375_M_Islet


title: DO-362_F_Islet


title: DO-361_F_Islet


title: AKR1B10 knockdown mice with BBR 4

city: Tianjin

first: Sa

last: Yang

address: 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District

institute: Tianjin University of Traditional Chinese Medicine

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sanple

source_name: Liver

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on anIllumina Novaseq™ 6000(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Liver

value: AKR1B10 knockdown


title: AKR1B10 knockdown mice with BBR 3


title: DO-360_F_Islet

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

value: pancreatic islet

value: 45% fat


title: AKR1B10 knockdown mice with BBR 1


title: AKR1B10 knockdown mice with BBR 2


title: AKR1B10 knockdown mice 4


title: DO-359_F_Islet


title: DO-358_F_Islet


title: DO-357_F_Islet


title: AKR1B10 knockdown mice 2


title: DO-356_F_Islet


title: DO-355_F_Islet


title: AKR1B10 knockdown mice 1


title: AKR1B10 knockdown mice 3


title: DO-354_F_Islet


title: DO-353_F_Islet


title: negative control mice with BBR 3

value: control


title: negative control mice with BBR 1


title: negative control mice with BBR 4


title: negative control mice with BBR 2


title: DO-348_F_Islet


title: negative control mice 4


title: DO-350_F_Islet


title: DO-346_F_Islet


title: negative control mice 3


title: DO-352_F_Islet


title: negative control mice 1


title: DO-347_F_Islet


title: DO-345_F_Islet


title: negative control mice 2


title: DO-344_F_Islet


title: DO-349_F_Islet


title: stimulated microglia no.4

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

country: Japan

institute: Tokai University

description: 12/16 IgG

data_processing:
Raw sequencing data were processed using Fastp version 0.23.2 for quality control, including adapter trimming and removal of low-quality reads.
Cleaned reads were aligned to the GRCm38 reference genome using HISAT2 version 2.2.1.
Alignment files were sorted and indexed using Samtools version 1.12.
Duplicate marking was done using Picard 2.26.3.
Read counting was conducted using R 4.1.2 with RsubRead 2.8.2 (FeatureCounts), and statistical analysis was carried out using edgeR 3.36.0.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: neocortex and hippocampus

growth_protocol: Mouse hippocampi and neocortices were mechanically dissociated and meninges removed with a 70 μm filter. Single cell suspensions from brains were pooled in poly-L-lysine-coated cell cultivation flasks in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin. The culture media was changed the next day to remove cell debris. Thereafter, the medium was changed every four days. After 12 days of culture, microglia were collected by shaking the flask at 200 rpm for 2 h. Detached microglia were then plated in a poly-L-lysine-coated 12-well plate and placed in a 37 °C incubator. These primary microglia were maintained in the new plates for 3 days before treatment.

extract_protocol:
Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA library for RNA-seq was prepared using NEBNext Ultra RNA Library Kit (Illumina) following manufacture's protocols.

treatment_protocol: IgG (10 µg/ml) treatment was performed at DIV15 for 24 h.

value: neocortex and hippocampus

value: microglia

value: wild-type

value: 10 µg/ml IgG for 24 hr.


title: stimulated microglia no.2

description: 12/2 IgG


title: stimulated microglia no.3

description: 12/9 IgG


title: stimulated microglia no.1

description: 10/21 IgG


title: DO-340_F_Islet


title: DO-338_F_Islet


title: untreated microglia no.3

description: 12/9 cont.

value: untreated


title: untreated microglia no.4

description: 12/16 cont.


title: untreated microglia no.2

description: 12/2 cont.


title: untreated microglia no.1

description: 10/21 cont.


title: DO-333_F_Islet


title: DO-335_F_Islet


title: DO-332_F_Islet


title: Striatum_6M_zQ175.Msh3.HOM_male_rep4

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
X182.Str
2x150bp configuration

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq 2 x 150 bp generating ~ 30M raw pair-end reads.
Input reads were trimmed and filtered using Omicsoft Array Studio, V11.3. The following filtering and trimming options were applied prior to alignment: ReadTrimQuality=2, FilterSource IlluminaAdapters, Human.rRNA, Human.tRNA, LengthCutoff=25, AverageQualityCutoff=10, PolyRateCutoff=80.
Reads from paired-end fastq files were aligned to Mouse.B38 (GRCm38) genome with Ensembl94 (GRCm38.p6) gene model using Omicsoft Array Studio, V11.3.
Raw counts and FPKM values were obtained by using Omicsoft Array Studio, V11.3.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Tab-delimited txt files include FPKM and count values for each Sample.

source_name: Corpus Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using Illumina RNA preparation with polyA selection.

value: Corpus Striatum

value: 6 months

tag: Sex

value: male

tag: sample id

tag: mouse id


title: Striatum_6M_zQ175.Msh3.HOM_male_rep3

description:
X181.Str
2x150bp configuration


title: Striatum_6M_zQ175.Msh3.HOM_male_rep5

description:
X310.Str
2x150bp configuration


title: DO-342_F_Islet


title: DO-329_F_Islet


title: DO-328_F_Islet


title: DO-343_F_Islet


title: Striatum_6M_zQ175_male_rep4

description:
X378.Str
2x150bp configuration


title: DO-330_F_Islet


title: Striatum_6M_zQ175_female_rep4

description:
X334.Str
2x150bp configuration

value: female


title: Striatum_6M_zQ175.Msh3.HOM_male_rep2

description:
X171.Str
2x150bp configuration


title: DO-327_F_Islet


title: Striatum_6M_WT_female_rep4

description:
X178.Str
2x150bp configuration

value: Wild Type


title: Striatum_6M_WT_female_rep3

description:
X161.Str
2x150bp configuration


title: DO-326_F_Islet


title: DO-339_F_Islet


title: DO-325_F_Islet


title: Striatum_6M_zQ175_male_rep2

description:
X138.Str
2x150bp configuration


title: Striatum_6M_zQ175_female_rep3

description:
X127.Str
2x150bp configuration


title: DO-337_F_Islet


title: DO-324_F_Islet


title: DO-323_F_Islet


title: DO-336_F_Islet


title: Striatum_6M_WT.Msh3.HOM_female_rep4

description:
X93.Str
2x150bp configuration


title: Striatum_6M_zQ175_male_rep3

description:
X370.Str
2x150bp configuration


title: DO-322_F_Islet


title: DO-331_F_Islet


title: Striatum_6M_WT.Msh3.HOM_female_rep3

description:
X86.Str
2x150bp configuration


title: DO-321_F_Islet


title: DO-320_M_Islet


title: Striatum_6M_zQ175.Msh3.HOM_female_rep2

description:
X85.Str
2x150bp configuration


title: DO-319_M_Islet


title: DO-318_M_Islet


title: Striatum_6M_WT.Msh3.HOM_female_rep2

description:
X63.Str
2x150bp configuration


title: Striatum_6M_WT.Msh3.HOM_male_rep4

description:
X75.Str
2x150bp configuration


title: Striatum_6M_zQ175_male_rep1

description:
X46.Str
2x150bp configuration


title: DO-317_M_Islet


title: DO-315_M_Islet


title: Striatum_6M_WT.Msh3.HOM_male_rep3

description:
X31.Str
2x150bp configuration


title: DO-314_M_Islet


title: DO-316_M_Islet


title: Striatum_6M_WT_female_rep2

description:
X56.Str
2x150bp configuration


title: Striatum_6M_zQ175.Msh3.HOM_female_rep3

description:
X109.Str
2x150bp configuration


title: Striatum_6M_WT_male_rep3

description:
X30.Str
2x150bp configuration


title: DO-312_M_Islet


title: DO-313_M_Islet


title: DO-311_M_Islet


title: Striatum_6M_zQ175.Msh3.HOM_female_rep1

description:
X28.Str
2x150bp configuration


title: DO-310_M_Islet


title: Striatum_6M_zQ175_female_rep1

description:
X25.Str
2x150bp configuration


title: Striatum_6M_WT_male_rep1

description:
X17.Str
2x150bp configuration


title: Striatum_6M_WT_male_rep2

description:
X23.Str
2x150bp configuration


title: DO-308_M_Islet


title: Striatum_6M_zQ175.Msh3.HOM_male_rep1

description:
X16.Str
2x150bp configuration


title: Striatum_6M_WT_male_rep4

description:
X38.Str
2x150bp configuration


title: DO-307_M_Islet


title: Striatum_6M_WT.Msh3.HOM_female_rep1

description:
X4.Str
2x150bp configuration


title: DO-305_M_Islet


title: DO-306_M_Islet


title: Striatum_6M_WT_female_rep1

description:
X10.Str
2x150bp configuration


title: DO-304_M_Islet


title: Striatum_6M_zQ175_female_rep2

description:
X27.Str
2x150bp configuration


title: EU_G

city: Lausanne

first: Flora

last: Brozzi

address: Rue du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

description: Row counts and normalized counts

library_source: other

data_processing:
For each read, the 3' Adapter was removed to extract the captured RNA molecule sequence (the leading part of the read up to the adapter). Then the Primer site was located and the 12 nucleotides UMI extracted.  Then the the 6 nucleotide barcode was compared to the expected barcode(s) of the samples. If the 3' adapter, primer and barcode have been correctly recognised, the sequence is kept to record the number of different UMIs observed.
Only sequences 16-55 nucleotides long, with at least 5 counts in at least 4 samples were retained
Sequences that could originate from fragments of the 400 "high confidence" and 7 "notable atypical predictions" tRNA sequences retrieved from http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc39/ or be fragments of the control miR-238 C.elegans sequence spiked in each samples were retained
Differential expression analysis was performed with R (version 4.2.2) and DEseq2 (version 1.38.3; ref 1) using default parameters.
Assembly: 400 "high confidence" and 7 "notable atypical predictions" tRNA sequences retrieved from http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc39/
Supplementary files format and content: excel table sorted by adjusted pValue with samples raw counts, DEseq2 normalised counts, and rlog counts after applying a variance stabilising transformation (VST) using the vst function taking into account the experimental design (blind=FALSE). Foldchange computed by DEseq2 and moderated by the lfcShrink function using the apeglm (ref 2) shrinkage estimator are also provided in columns FoldChange and FoldChange_apeglm, respectively.

molecule: other

source_name: Islets of Langerhans

growth_protocol: Pancreatic β-cells were isolated from female NOD.CB-17-Prkdc scid/Rj (NOD.SCID) mice after T-cell adoptive transfer.  In average, 3-4*106 T-cells were injected in the tail vein of each recipient NOD.SCID mouse. Control mice were injected with the same volume of saline solution, without T-cells (CTRL). 48h after T cell injection, mice were sacrificed, and islet cells isolated. Mouse pancreases were digested with collagenase (Sigma), and islets isolated by Histopaque (Sigma) density gradient and handpicking. Purified islet cells were cultured in RPMI 1640 GlutaMAX medium (ThermoFisher) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin, 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma). After 2h islets were dissociated into single cells by incubation in Ca2+/Mg2+ free phosphate-buffered saline, 3 mM EGTA, and 0.002% trypsin (ThermoFisher) for 2-3 min at 37 °C. Fractions enriched of β-cells were obtained by Fluorescence-Activated Cell Sorting (FACS) of dissociated islet cells based on β-cell autofluorescence as previously described (Stange, G. et al, Methods Mol. Med. 2003). Dissociated islet cells were washed once with FACS buffer (0.1% BSA, 2mM EDTA, 11mM glucose in PBS) and incubated for 5 minutes with TruStain FcX™ (anti-mouse CD16/32) Antibody (BioLegend), at 4°C. Then cells were incubated for 30 min in the dark at 4°C with the following antibodies: 1:200 of FITC anti-CD45 (BioLegend 157213), 1:40 of APC anti-CD3 (BioLegend 100235), 1:20 of Brilliant Violet 421 anti-CD4 (BioLegend 100437), and 1:20 of PE anti-CD25 (BioLegend 102007). Cells were then washed twice with FACS buffer and analysed by FCF-Aria-II (SORP). FAC-sorted Pancreatic β-cells were purified from the CD45-negative fraction based on β-cell autofluorescence (see above) and directly collected on Qiazol (Qiagen).

extract_protocol:
RNA of FACS-sorted β-cells  was extracted with the miRNeasy kit (Qiagen) and EU-tagged RNA was biotinylated and pulled down using the Click-iT Nascent RNA Capture kit (Thermo Fisher C10365). For each condition, the same amount of RNA was incubated with streptavidin-coated beads and, after washing, the biotinylated RNA attached to the beads was eluted using the following Elution Solution: 95% Formamide, 10 mM EDTA in H2O. Eluted RNA was purified again with the miRNeasy kit and used for library preparation.
Libraries were prepared with QIAseq miRNA Library Kit (Qiagen) following manufacter's protocol.

treatment_protocol: A particular treatment was performed on the T-cells injected on NOD.SCID mice. CD4+/CD25- T-cells from NOD.Cg-Tg (TcraBDC2.5, TcrbBDC2.5) mice were isolated, activated, and treated for 48h with 200 μM of Ethynyl Uridine. The cells were then washed three times with PBS and resuspended in sterile saline solution (Sigma), before the intravenal injection on NOD.SCID mice.

value: Islets of Langerhans

value: 8-12 weeks

value: FACS-sorted Beta-cells

value: NOD.CB-17-Prkdc scid/Rj mice


title: Striatum_6M_WT.Msh3.HOM_male_rep1

description:
X2.Str
2x150bp configuration


title: DO-303_M_Islet

value: pancreatic islet


title: DO-302_M_Islet

value: 45% fat


title: DO-299_M_Islet


title: DO-301_M_Islet


title: EU_D

description: Row counts and normalized counts


title: EU_C

description: Row counts and normalized counts


title: DO-309_M_Islet


title: DO-300_M_Islet


title: DO-297_M_Islet


title: CT_H

description: Row counts and normalized counts


title: DO-298_M_Islet


title: DO-296_M_Islet


title: EU_A

description: Row counts and normalized counts


title: CT_G

description: Row counts and normalized counts


title: CT_D

description: Row counts and normalized counts


title: CT_C

description: Row counts and normalized counts


title: DO-295_M_Islet


title: Striatum_6M_WT.Msh3.HOM_male_rep2

description:
X14.Str
2x150bp configuration


title: DO-294_M_Islet


title: CT_A

description: Row counts and normalized counts


title: EU_H

description: Row counts and normalized counts


title: DO-292_M_Islet


title: O_Phe

description: Expression values

data_processing:
The analysis was performed using the QIAGEN RNA-seq Analysis Portal 4.1
Assembly: GRCm38
Supplementary files format and content: tab-delimited xlsx files include RNA TPM, RPKM and CPM values

growth_protocol: Mouse pancreases from C57BL/6NRj mice were digested with collagenase (Sigma), and islets isolated by Histopaque (Sigma) density gradient and handpicking. Purified islet cells were cultured in RPMI 1640 GlutaMAX medium (ThermoFisher) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin, 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma). Rodent islets were dissociated into single cells by incubation in Ca2+/Mg2+free phosphate-buffered saline, 3 mM EGTA, and 0.002% trypsin (ThermoFisher) for 2-3 min at 37 °C and cultured 24h before treatment.

extract_protocol:
RNA was extracted with miRNeasy kit (Qiagen).
Illumina stranded mRNA prep

treatment_protocol: Dissociated mouse islet cells were transfected using Lipofectamine 2000 (Thermo Fisher) with scramble control oligonucleotides or specific tRF mimics for LysCTT-5’, PheGAA-5’ and SerGCT-3’  (Integrated DNA Technologies). RNA was collected in Qiazol (Qiagen), 48h after transfection

value: Beta-cells and alpha-cells mainly

value: C57BL/6NRj mice


title: P_Ser

description: Expression values


title: DO-290_M_Islet


title: DO-291_M_Islet


title: M_CT

description: Expression values

value: Control


title: N_Lys

description: Expression values


title: L_Ser

description: Expression values


title: DO-287_M_Islet


title: DO-289_M_Islet


title: K_Phe

description: Expression values


title: DO-285_M_Islet


title: I_CT

description: Expression values


title: H_Ser

description: Expression values


title: DO-286_M_Islet


title: G_Phe

description: Expression values


title: J_Lys

description: Expression values


title: DO-284_M_Islet


title: DO-283_M_Islet


title: E_CT

description: Expression values


title: D_Ser

description: Expression values


title: DO-281_M_Islet


title: C_Phe

description: Expression values


title: DO-280_M_Islet


title: DO-293_M_Islet


title: DO-279_M_Islet


title: B_Lys

description: Expression values


title: DO-278_M_Islet


title: A_CT

description: Expression values


title: DO-277_M_Islet


title: DO-288_M_Islet


title: DO-275_M_Islet


title: 324RFP

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

library_source: genomic

data_processing:
The fastq files were aligned to the mouse reference GRCm38/mm10 sequence using bwa (v 0.7.15) mem with default parameters.
The technique duplicates were merged and library PCR duplicates were removed with picard (v 2.18.7).
SNPs were called from the individual strain BAM files with Genome Analysis Toolkit (v4.0.5.1).
The SNPs were filtered with expression “QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0”
and the Indels were filtered with expression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"
Assembly: GRCm38/mm10
Supplementary files format and content: vcf files with merged SNPs and Indels
Library strategy: Whole genome sequencing (WGS)

molecule: genomic DNA

source_name: sarcoma

extract_protocol:
genomic DNA extraction using Qiagen Dneasy kit
We do not know, need input from Core

value: sarcoma

value: Sorted sarcoma cells

value: FACS sorted from primary mouse sarcoma


title: 324C+R


title: 324CFP


title: DO-282_M_Islet

first: Gary

last: Churchill

address: 600 Main St

institute: The Jackson Laboratory


title: DO-274_M_Islet


title: DO-272_M_Islet


title: 732RFP


title: 324YFP


title: F_Lys

description: Expression values


title: 277GFP


title: 732CFP


title: 732YFP


title: DO-271_M_Islet


title: 277YFP


title: DO-269_F_Islet


title: DO-268_F_Islet


title: Metastatic mouse UPS cell lacking Setd1a, IgG, rep3

data_processing:
ChIP-seq reads were trimmed using TrimGalore (v 0.6.6) and then aligned to GRCm38/mm10 reference genome by bwa (v 0.7.17-r1188).
Unmapped reads reads aligned to multiple locations were removed using samtools (v 1.11).
Duplicated reads were marked by picard (v 2.26.0).
The genomic coverage was saved in bigwig format and normalized by CPM method by bedTools (v 2.29.2) and UCSC Utilities bedGraphToBigWig (v 377).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig normalized by total reads

source_name: Mouse Setd1a KO UPS cell

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the SimpleChIP Plus Sonication Chromatin IP kit (CST). 10 ug of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit and 2% Agarose gel

value: Mouse Setd1a KO UPS cell

tag: chip antibody

value: IgG


title: 277RFP

tag: tissue


title: DO-266_F_Islet

tag: diet


title: DO-267_F_Islet


title: Metastatic mouse UPS cell lacking Setd1a, IgG, rep2


title: DO-265_F_Islet


title: Metastatic mouse UPS cell lacking Setd1a, IgG, rep1


title: DO-276_M_Islet


title: Metastatic mouse UPS cell, IgG, rep3

source_name: mouse UPS cell

value: mouse UPS cell


title: DO-263_F_Islet


title: DO-273_M_Islet


title: Metastatic mouse UPS cell, IgG, rep2


title: Metastatic mouse UPS cell, IgG, rep1


title: DO-270_F_Islet


title: DO-262_F_Islet


title: DO-260_F_Islet


title: DO-261_F_Islet


title: Metastatic mouse UPS cell lacking Setd1a, H3K4Me3, rep2


title: DO-259_F_Islet


title: Metastatic mouse UPS cell lacking Setd1a, H3K4Me3, rep1


title: DO-258_F_Islet


title: Metastatic mouse UPS cell, H3K4Me3, rep2


title: Metastatic mouse UPS cell, H3K4Me3, rep1


title: DO-256_F_Islet


title: DO-257_F_Islet


title: DO-255_F_Islet


title: Lane4_Sample_50

city: Columbus

first: Russell

last: Ault

state: OH

address: 370 W 9th Ave

institute: The Ohio State University College of Medicine

data_processing:
Basecalls performed using bcl2fastq2 v.2.19
Adapter removal and quality trimming were performed by using Trim Galore! v.0.6.4
Alignment performed by BitMapperBS v.1.0.2.3 with default options: bitmapperBS --search ${REFERENCE} --seq1 ${R1} --seq2 ${R2} --bam -o Sample_${n}.bam
Methylation levels were determined using MethylDackel v.0.4.0 with default options: MethylDackel extract $DACKELREFERENCE $bam_file
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Processed files are MethylDackel bedGraph output files with 1. Chromosome name 2. Start coordinate 3. End coordinate 4. Methylation percentage 5. Number of alignments reporting methylated bases 6. Number of alignments reporting unmethylated bases

source_name: Whole Blood

extract_protocol:
Whole blood was collected, mixed with EDTA, and mixed with Zymo Research DNA/RNA Shield. DNA was isolated using the Zymo Research Quick-DNA kit and Genomic DNA Clean & Concentrator kit.
Libraries were prepared using Reduced Representation Bisulfite Sequencing. 52 samples were pooled together using custom synthesized methylated adapters with unique dual indexes (Integrated DNA Technologies).

value: Whole Blood

tag: mouse

tag: cage

value: infected

tag: strain

value: Heart


title: DO-254_F_Islet

city: Bar Harbor


title: Lane4_Sample_51

value: Balb/c


title: DO-253_F_Islet


title: Lane4_Sample_48

value: naive


title: Lane4_Sample_49


title: DO-264_F_Islet


title: DO-251_F_Islet


title: Lane4_Sample_46


title: DO-252_F_Islet


title: Lane4_Sample_45


title: Lane4_Sample_43


title: DO-250_F_Islet


title: Lane4_Sample_44


title: DO-249_F_Islet


title: Lane4_Sample_41


title: Lane4_Sample_40


title: DO-245_F_Islet


title: DO-244_F_Islet


title: Lane4_Sample_39


title: Lane4_Sample_52


title: DO-247_F_Islet


title: DO-242_F_Islet


title: Lane4_Sample_42


title: DO-243_F_Islet


title: Lane4_Sample_38


title: Lane4_Sample_37


title: Lane4_Sample_35


title: Lane4_Sample_36


title: DO-239_F_Islet


title: DO-240_F_Islet


title: Lane4_Sample_33


title: DO-238_F_Islet


title: Lane4_Sample_34


title: DO-241_F_Islet


title: DO-236_F_Islet


title: Lane4_Sample_32


title: DO-235_F_Islet


title: DO-237_F_Islet


title: DO-246_F_Islet


title: Lane4_Sample_31


title: DO-234_F_Islet


title: DO-233_F_Islet


title: Lane4_Sample_29


title: Lane4_Sample_28


title: DO-230_F_Islet


title: Lane4_Sample_25


title: DO-229_F_Islet


title: DO-232_F_Islet


title: Lane4_Sample_27


title: Lane4_Sample_26


title: Lane4_Sample_24


title: DO-231_F_Islet


title: DO-228_F_Islet


title: DO-226_F_Islet


title: Lane4_Sample_22


title: DO-227_F_Islet


title: Lane4_Sample_21


title: Lane4_Sample_19


title: DO-224_F_Islet


title: DO-225_F_Islet


title: DO-223_F_Islet


title: Lane4_Sample_18


title: Lane4_Sample_30


title: DO-222_F_Islet


title: Lane4_Sample_17


title: DO-221_F_Islet


title: Lane4_Sample_16


title: DO-220_M_Islet


title: DO-219_M_Islet


title: Lane4_Sample_14


title: Lane4_Sample_13


title: Lane4_Sample_23


title: Lane4_Sample_12


title: DO-216_M_Islet


title: DO-217_M_Islet


title: DO-215_M_Islet


title: Lane4_Sample_11


title: Lane4_Sample_10


title: Lane4_Sample_20


title: Lane4_Sample_8


title: DO-212_M_Islet


title: Lane4_Sample_7


title: DO-209_M_Islet


title: DO-210_M_Islet


title: Lane4_Sample_4


title: DO-208_M_Islet


title: Lane4_Sample_9


title: Lane4_Sample_15


title: DO-218_M_Islet


title: Lane4_Sample_5


title: DO-214_M_Islet


title: Lane4_Sample_2


title: DO-206_M_Islet


title: DO-211_M_Islet


title: Lane4_Sample_1


title: DO-205_M_Islet


title: Lane3_Sample_52


title: Lane4_Sample_3

value: IVC


title: Lane4_Sample_6


title: DO-204_M_Islet

value: pancreatic islet


title: Lane3_Sample_51


title: DO-203_M_Islet

value: 45% fat


title: DO-207_M_Islet


title: Lane3_Sample_49


title: DO-213_M_Islet


title: DO-201_M_Islet


title: DO-200_M_Islet


title: Lane3_Sample_47


title: Lane3_Sample_48


title: Lane3_Sample_45


title: Lane3_Sample_46


title: DO-197_M_Islet


title: DO-196_M_Islet


title: Lane3_Sample_44


title: DO-194_M_Islet


title: Lane3_Sample_43


title: DO-193_M_Islet


title: Lane3_Sample_42


title: DO-192_M_Islet


title: DO-191_F_Islet


title: Lane3_Sample_41


title: DO-190_M_Islet


title: DO-189_M_Islet


title: Lane3_Sample_50


title: Lane3_Sample_40


title: DO-187_M_Islet


title: Lane3_Sample_39


title: DO-188_M_Islet


title: DO-185_M_Islet


title: DO-199_M_Islet


title: DO-186_M_Islet


title: Lane3_Sample_38


title: DO-184_M_Islet


title: DO-183_M_Islet


title: DO-182_M_Islet


title: DO-181_M_Islet


title: DO-180_M_Islet


title: DO-179_M_Islet


title: DO-178_M_Islet


title: Lane3_Sample_36


title: Lane3_Sample_35


title: DO-202_M_Islet


title: DO-177_M_Islet


title: DO-175_M_Islet


title: Lane3_Sample_33


title: DO-176_M_Islet


title: DO-174_M_Islet


title: DO-173_M_Islet


title: Lane3_Sample_37


title: Lane3_Sample_32


title: DO-171_M_Islet


title: DO-170_F_Islet


title: Lane3_Sample_30


title: DO-169_F_Islet


title: Lane3_Sample_34


title: DO-168_F_Islet


title: Lane3_Sample_31


title: DO-167_F_Islet


title: DO-172_M_Islet


title: Lane3_Sample_28


title: DO-165_F_Islet


title: DO-166_F_Islet


title: DO-163_F_Islet


title: Lane3_Sample_27


title: DO-162_F_Islet


title: Lane3_Sample_29


title: DO-195_M_Islet


title: Lane3_Sample_26


title: DO-164_F_Islet


title: Lane3_Sample_25


title: Lane3_Sample_23


title: shH3_2_48_3

city: cincinnati

first: XUEZHAO

last: LIU

institute: cincinnati children's hospital medical center

data_processing:
All RNA-seq data were aligned to mm9 or Rn5 using TopHat with default settings (http://tophat.cbcb.umd.edu/). We used Cuff-diff to (i) estimate fragments per kilobase of transcript per million mapped read (FPKM) values for known transcripts and to (ii) analyze differentially expressed transcripts. In all differential expression tests, a difference was considered significant if the p value was less than 0.05.
Assembly: mm10/rn5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: brain

value: primary iOLs

tag: cell type

value: oligodendrocytes

tag: genotype

value: wildtype

tag: treatment


title: DO-161_F_Islet


title: Lane3_Sample_22


title: shH3-2_48-2

tag: cell line


title: DO-159_F_Islet


title: DO-158_F_Islet


title: DO-160_F_Islet


title: Lane3_Sample_24


title: Lane3_Sample_21


title: DO-157_F_Islet


title: shH3_1_48_3


title: DO-155_F_Islet


title: DO-156_F_Islet


title: HDAC12i_h3k27ac_X8

data_processing:
All sequencing data were mapped to rat genome rn5 and peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) version 1.4.2 (http://liulab.dfci.harvard.edu/MACS) with a P value cutoff of 1 x e-9 to obtain raw binding peaks
Assembly: rn5
Supplementary files format and content: wig,bigwig
Library strategy: Cut&Run

extract_protocol:
Cut &Run cleaved fragments were purified by Qiagen MinElute PCR Purification Kit.
Libraries were prepared for Illumina sequencing with Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

tag: antibody


title: shC_48_2_2

value: lenti-shcontrol


title: Lane3_Sample_19


title: Lane3_Sample_20


title: shH3_1_48_1_2


title: dmso_h3k2k27ac_X2

value: DMSO


title: Lane3_Sample_18


title: Group-III 8B2 BUCCAL

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95230.gif

hyb_protocol: not provided

scan_protocol: scanner model: G2505C

data_processing: VALUE is Log RED/GREEN

organism: Macaca mulatta

source_name: 825 ng of amplified monkey POOLED Group I Buccal cDNA

label_protocol: not provided

extract_protocol: not provided

tag: tissue type

value: Oropharyngeal mucosal tissue

tag: infection

value: control

source_name: 825 ng of amplified monkey Group-III 8B2 BUCCAL cDNA

value: SIV

tag: individual


title: 26C_H3K9me3


title: ChIPseq_H3K4me3_Input_sticklebackTestesPool_Marine

city: Tuebingen

first: Felicity

middle: C

last: Jones

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory of the Max Planck Society

data_processing:
ChIPseq reads were trimmed to 40 bp using Trimmomatic (Bolger et al 2014 Bioinformatics 30:2114-20).
For DMC1 ChIP a specialized bioinformatic pipeline described in Khil et al (2012) Genome Research 22:957-65 was used to process paired-end sequencing data and extract 'Type 1' sequencing reads obtained from pulldown of DMC1-bound single stranded DNA.  This generated bedfiles used as input for MACS2 peak calling (described below).  This was not performed for H3K4me3 ChIPseq.
MACS2 (v2.1.1) was used to call peaks from DMC1 'Type 1' reads relative to DMC1 kinetic enrichment ChIP Input controls. (v2.1.1) with the following parameters: -q 0.1 --nomodel --slocal 5000 --llocal 10000 --extsize 800 -f BED --SPMR -g 463000000 -B. For H3K4me3 ChIP reads, macs2 peak calling was performed using default parameters.
ChIPseq normalized treatment coverage plots (DMC1 or H3K4me3 ChIP) and control (kinetic enrichment control, or H3K4me3 ChIPseq input control) coverage plots were generated using MACS2. narrowPeak files were generated using MACS2
Assembly: Broad/gasAcu1
Supplementary files format and content: bed (representing 'Type 1' DMC1-bound single stranded DNA reads used as input for MACS2; only for DMC1 ChIPseq), bedGraph (from MACS2 ChIPseq treatment and input controls), peak files (except for ChIP input samples)

organism: Gasterosteus aculeatus

source_name: TestesPool

growth_protocol: Wild-derived strains of marine and freshwater sticklebacks from the River Tyne, East Lothian, Scotland under a seasonally varying day length (3 months of 16 hours light, 8 hours dark, followed by 3 months of winter 8 hours dark, 16 hours light).  Juvenile sticklebacks were reared from fertilisation under 3 months of summer light cycle followed by 3 months of winter light cycle.  Testes and livers were collected during the last three weeks of the 3-month low light period, snap-frozen in liquid nitrogen, and stored in -80’C.

extract_protocol:
Tissue lysate was prepared from frozen tissue following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65.
The ChIP pulldown of DMC1-bound single stranded DNA was performed with "kinetic enrichment" following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65 and was followed sequentially by a ChIP pull down H3K4me3 on the same tissue lysate.

value: TestesPool

value: wild-derived marine strain


title: DO-152_F_Islet

source_name: pancreatic islet


title: Group-IV 4882 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95234.gif

source_name: 825 ng of amplified monkey Group-IV 4882 BUCCAL cDNA

value: LCV SIV


title: Group-IV 929 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95236.gif

source_name: 825 ng of amplified monkey Group-IV 929 BUCCAL cDNA


title: DO-153_F_Islet


title: Group-IV A5V048 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95245.gif

source_name: 825 ng of amplified monkey Group-IV A5V048 BUCCAL cDNA


title: Group-III 4426 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95231.gif

source_name: 825 ng of amplified monkey Group-III 4426 BUCCAL cDNA


title: Group-IV 936 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95239.gif

source_name: 825 ng of amplified monkey Group-IV 936 BUCCAL cDNA


title: shC_48_1_2


title: DMSO_H3K9me3


title: Group-II DBXC BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95229.gif

source_name: 825 ng of amplified monkey Group II DBXC BUCCAL cDNA

value: LCV

value: DBXC


title: DO-151_F_Islet


title: Lane3_Sample_15

value: Whole Blood

value: infected

value: Balb/c

value: Heart


title: DMSO_H3K27me3

value: brain

value: primary iOLs


title: DO-149_F_Islet

value: pancreatic islet

value: 45% fat


title: Lane3_Sample_14


title: Group-IV AP65 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95242.gif

source_name: 825 ng of amplified monkey Group-IV AP65 BUCCAL cDNA


title: Group-IV 926 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95235.gif

source_name: 825 ng of amplified monkey Group-IV 926 BUCCAL cDNA


title: Group-IV 937 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95240.gif

source_name: 825 ng of amplified monkey Group-IV 937 BUCCAL cDNA


title: ChIPseq_DMC1_KEInput_sticklebackTestesPool_Marine


title: Group-II DCOC BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95226.gif

source_name: 825 ng of amplified monkey Group II DCOC BUCCAL cDNA

value: DCOC


title: DO-150_F_Islet


title: Group-II DCOD BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95227.gif

value: Oropharyngeal mucosal tissue

source_name: 825 ng of amplified monkey Group II DCOD BUCCAL cDNA

value: DCOD


title: ChIPseq_H3K4me3_sticklebackTestesPool_Marine


title: ChIPseq_DMC1_KEInput_sticklebackLiverPool_Freshwater

source_name: LiverPool

value: LiverPool

value: wild-derived freshwater strain


title: Lane3_Sample_13

source_name: Whole Blood


title: DO-148_F_Islet


title: 26C_H3K27AC

source_name: brain

value: oligodendrocytes

value: wildtype


title: ChIPseq_DMC1_sticklebackLiverPool_Freshwater


title: DO-154_F_Islet


title: Group-IV 932 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95237.gif

source_name: 825 ng of amplified monkey POOLED Group I Buccal cDNA

value: control

source_name: 825 ng of amplified monkey Group-IV 932 BUCCAL cDNA

value: LCV SIV


title: Group-IV 4B7 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95241.gif

source_name: 825 ng of amplified monkey Group-IV 4B7 BUCCAL cDNA


title: Lane3_Sample_12

value: Whole Blood

value: naive


title: Lane3_Sample_11

value: Balb/c


title: DMSO_H3K27AC

value: DMSO


title: ChIPseq_DMC1_sticklebackTestesPool_Marine

source_name: TestesPool

value: TestesPool

value: wild-derived marine strain


title: rat_iOL_DMSO

data_processing:
MAPS pipeline was used to analyze H3K27ac HiChIP data generated from control and 26C treated oligodendrocyte cells. Briefly, we mapped the raw fastq files to the reference genome rn5 using bwa-mem and kept only the uniquely mapped reads. We then kept paired-end reads where at least one end overlaps with the H3K27ac ChIP–seq peaks in the matched cell type and fitted a positive Poisson regression model to remove systematic biases including restriction enzyme cutting frequency, GC content, sequence uniqueness, and ChIP efficiency. We then identified significant long-range chromatin interactions as 10 kb bin pairs with FDR <1% and normalized chromatin contact frequency >2. Lastly, we assigned genes whose transcription start site resides in the anchor binsof MAPS-identified interactions
Assembly: rn5
Supplementary files format and content: txt file contains MAPS-identified interactions
Supplementary files format and content: txt file contains MAPS-identified interactions
Library strategy: HiChIP

extract_protocol:
~5 million rat iOL were treated with vehicle or 26C and then crosslinked with 1% formaldehyde for 10 min at room temperature and lysed with 1× Nuclease Digest Buffer. Chromatin was digested by Enzyme Mix and sonicated using Covaris sonicator then processed with chromatin immunoprecipitation using the H3K27ac antibody
The DNA libraries were amplified using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645, New England Biolabs) according to its recommended protocol and sequenced by NovaSeq 6000 system on pair-end 2×150 bp mode

value: brain

value: primary iOLs


title: rat_iOL_26c


title: DO-145_F_Islet

data_processing:
Assembly: GRCm38
Supplementary files format and content: DO_RNAseq_islet_counts_matrix.csv
Supplementary files format and content: DO_RNAseq_islet_mrna_annots.csv
Supplementary files format and content: DO_RNAseq_islet_vst_matrix.csv
Islet: processed DO islet RNAseq data (legacy data, reprocessed with batch effects removed as reported in /RNAseq/Raw/GBRS/QTLViewer_setup/QTLv_format_ISLET_REMOVE_BATCH.R script).
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.
counts_matrix.csv: raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.
vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
mrna_annots.csv: gene annotation file ENSEMBL version 75.
QTLViewer: QTLViewer data object and documentation. QTLViewer object generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
GBRS_QTL2_genoprobs: final genoprobs on QTL2 format generated through GBRS for each tissue (used for genotype QCing). Genoprobs generated by the R script /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_genoprobs.R

source_name: pancreatic islet

value: pancreatic islet

value: 45% fat


title: Lane3_Sample_17

value: infected

value: Heart


title: ChIPseq_DMC1_KEInput_sticklebackTestesPool_Freshwater

value: wild-derived freshwater strain


title: Lane3_Sample_10


title: Lane3_Sample_8


title: Dex 2

city: Valencia

first: Vicente

last: Balanzà

state: Valencia

address: Av de los Naranjos s/n

department: Development and hormonal action

country: Spain

institute: IBMCP (CSIC-UPV)

data_processing:
Paired-end sequencing (2 × 150 bp) was performed on a MiSeq (Illumina).
Reads were aligned to the reference genome of Arabidopsis thaliana available at the TAIR database (Lamesch et al., 2012) using TopHat (Trapnell et al., 2009) and Bowtie (Langmead et al., 2009) software.
The abundance estimation of the transcripts was performed using the RSEM package (Li and Dewey, 2011) and the differentially expressed transcripts (fragments per kilobase million value) were estimated using Cufflinks (Trapnell et al., 2010).
The sequences from DEG were annotated through BLAST search against the TAIR database
Assembly: Arabidopsis thaliana (TAIT10)
Supplementary files format and content: tab-delimited text file include tpm values for each sample

organism: Arabidopsis thaliana

source_name: Inflorescence meristem

growth_protocol: Plants were grown at 21°C under long day conditions (16 h light, 8h night), in a 2:1:1 by vol. mixture of peat:perlite:vermiculite.

extract_protocol:
RNA for RNA-seq was obtained with the RNeasy Plant Mini Kit (QUIAGEN)
The cDNA libraries were built using the Novogene Company United procedure for Illumina

treatment_protocol: Two weeks after bolting, inflorescence apexes of Arabidopsis 35S:LhG4:GR»HB21 (HB21 ind) plants were treated with dexamethasone, that allows the HB21 expression, or mock. 6-8 hours after treatment inflorescence apexes were collected removing all visible opened flowers.

value: Inflorescence meristem

tag: developmental stage

value: two weeks after bolting

value: dexamethasone

tag: time

value: 6 hours post-treatment


title: Lane3_Sample_9

value: Whole Blood


title: Group-III G415 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95232.gif

value: Oropharyngeal mucosal tissue

value: control

source_name: 825 ng of amplified monkey Group-III G415 BUCCAL cDNA

value: SIV


title: Dex 3


title: DO-146_F_Islet


title: DO-147_F_Islet


title: DO-143_F_Islet


title: Control and ACTN2 enh del

city: Baltimore

first: Emmanouil

last: Tampakakis

state: Maryland

address: 720 Rutland Ave, Ross 1033

department: Division of Cardiology

institute: Johns Hopkins School of Medicine

description: The samples were barcoded using Multi-seq and sequenced together

data_processing:
Samples are demultiplexed using the deMULTIplex package by Dr. Chris McGinnis from UCSF
Readings were mapped with STAR and featureCounts-based zUMIs
Assembly: GRCh38
Supplementary files format and content: matrix files
Supplementary files format and content: sample_groups.csv matches cell barcodes to the corresponding sample group after sample demultiplexing. Note that "Bar3" is the control group and Bar1 is the ACTN2 enhancer KO group as analyzed in this study.

source_name: hPSC-CMs

extract_protocol:
Day 25 hPSC-CMs were dissociated using TrypLE (Gibco), single cells were harvested and sorted using the droplet based 10x Genomics Chromium system.
RNA-seq cDNA libraries were generated using the Chromium Next Gem Single Cell Kit (10x Genomics)

tag: cell line_source

value: human pluripotent stem cells (hPSCs) (H9)

value: hPSC-CMs

value: Control and ACTN2 enh del


title: DO-144_F_Islet


title: Group-III G430 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95233.gif

source_name: 825 ng of amplified monkey Group-III G430 BUCCAL cDNA


title: SS_IMR90

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

description: HiC data

data_processing:
Hi-C datasets were processed using HiC-Pro (Version 3.1.0) with GATCGATC(MboI) ligation site. The duplicate reads and the invalid interactions were removed.
hicpro2juicebox tool to generate Juicebox-compatible files and Juicer tools software (Version 1.22.01) was used for visualization.
Assembly: hg38
Supplementary files format and content: .hic

source_name: IMR-90 cell line

growth_protocol: IMR-90 fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)

extract_protocol:
Crosslink 1 million cells with 37% formaldehyde(sigma, F8775) to a final concentration of 1% and incubate for 10 min at room temperature. Add glycine(Yuanye, S20159) to a final concentration of 0.125M, and terminate the formaldehyde crosslinking reaction at room temperature for 5 min. Cells were pelleted by spinning at 400g for 5 min at 4°C. The pellet was washed with cold PBS. Liquid nitrogen quick-freeze, placed at -80 degrees for reserve.fixed cells were incubated in 500μl of cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal CA630 and protease inhibitors (MCE-HY-K0010)) on ice for 25 min. Cells were pelleted by spinning at 400g for 5 min at 4°C. The pellet was washed twice with 1xNEBuffer2. Cells were resuspended in 50μl of 0.5%SDS and incubated for 8 min at 62°C. Next, reactions were terminated with 145μl of water and 25μl of 10%Triton X-100 (Sigma, 93443) at 37°C for 15min. Sample was digested overnight with 25μl of 10X NEBuffer2 and 20μl of MboI(NEB, R0147, 5U/µl) at 37 °C with rotation. Incubate the reactants at 62°C for 20min to inactivate MboI, then cold to room temperature.To complement the bases at the sticky end and label biotin at the DNA end, add 50μl of the mixture（37.5μl 0.4 mM biotin-14-dATP, 1.5μl of 10mMdCTP, 1.5μl of 10mM dGTP, 1.5μlof 10mM dTTP, and 8μl of 5U/μl DNA polymerase I, large (Klenow) fragment(NEB M0210)）and incubating at 37°C for 4h. After that, ligation is performed by adding 120μl of 10XNEB T4 DNA ligase buffer(NEB,B0202L), 100μl of 10% Triton X-100, 637.8μl of water, 1.2μl of 10%BSA(Sigma-Aldrich SRE0098) and 5μl of 400 U/μl T4 DNA ligase(NEB,M0202L) and incubating for 6h at room temperature. De-crosslinking was performed by adding 50μL of 20mg/mL proteinase K (NEB, P8107) and 120μL of 10%SDS incubate at 55°C for 30min. And then 130μL of 5M NaCl was added and incubated at 68 °C overnight. Samples were cooled to room temperature and divided into three equal portions. Then, 800μl of pure ethanol and 50μl of 3M sodium acetate pH5.2 were added to each tube which were subsequently incubated for 30 min at -80°C. Spin the tubes at maximum speed for 15 min at 4°C and wash twice with 70% ethanol. Resuspend the resulting pellet in 130μl of 10mM Tris-HCl, pH8.0 and incubate at 37 °C for 15 min.DNA was sheared using an ME220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp. Sheared DNA was size selected using VAHTS® DNA Clean Beads N411. Elution was done with hot (65°C) 70μl EB buffer. Next, the sample is transferred to a DNA LoBind tube (Eppendorf, 30108418) for related experimental manipulation. Take 150ul of T1 beads (MyOne Streptavin T1 Beads, Invitrogen, 65601) into a DNA LoBind Tubes and add 500ul 1x TWB buffer (5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20) wash twice. Resuspend the T1 beads with 70ul 2× Binding Buffer (10mM Tris-HCl (pH 7.5), 1mM EDTA, 2M NaCl) and combined with 70μl Hi-C DNA from the previous step. The mixture was incubated at room temperature for 15min . After which the magnet adsorbed to remove the supernatant; Wash twice with 200ul 1x TWB buffer and once with 200ul EB buffer. Finally, resuspend the beads with 50ul of water and transfer to a 200ul PCR tube.
Library construction using the VAHTS Universal DNA Library Prep Kit (Vazyme ND607) and VAHTS Multiplex Oligos Set 4/5 kits (Vazyme N321/N322) according to manufacturer’s instructions

treatment_protocol: overexpression by lentiviral infection.

value: IMR-90 cell line

value: fibroblasts

value: wild type

value: SS18-SSX1 overexpression


title: MUT_IMR90

description: HiC data

value: SS18(YA)-SSX1 mutant overexpression


title: Lane3_Sample_6

value: infected

value: Heart


title: Dex 1

value: Inflorescence meristem

value: two weeks after bolting


title: DO-141_F_Islet

value: pancreatic islet

value: 45% fat


title: DO-142_F_Islet


title: SS18_IMR90

description: HiC data

value: SS18 overexpression


title: SS-HDAC2

description: ChIP

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
Supplementary files format and content: bw

source_name: BJ

growth_protocol: fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions

value: BJ


title: mock 2

value: mock

value: 6 hours post-treatment